[2023-03-17 09:59:00,836] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:59:00,838] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:59:00,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference
[2023-03-17 09:59:02,026] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:59:02,027] [INFO] Task started: Prodigal
[2023-03-17 09:59:02,027] [INFO] Running command: cat /var/lib/cwl/stg1d08453b-3029-40f6-a1a6-c1681cedeb9e/OceanDNA-b21693.fa | prodigal -d OceanDNA-b21693/cds.fna -a OceanDNA-b21693/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:59:08,484] [INFO] Task succeeded: Prodigal
[2023-03-17 09:59:08,484] [INFO] Task started: HMMsearch
[2023-03-17 09:59:08,484] [INFO] Running command: hmmsearch --tblout OceanDNA-b21693/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference/reference_markers.hmm OceanDNA-b21693/protein.faa > /dev/null
[2023-03-17 09:59:08,643] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:59:08,644] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d08453b-3029-40f6-a1a6-c1681cedeb9e/OceanDNA-b21693.fa]
[2023-03-17 09:59:08,687] [INFO] Query marker FASTA was written to OceanDNA-b21693/markers.fasta
[2023-03-17 09:59:08,687] [INFO] Task started: Blastn
[2023-03-17 09:59:08,687] [INFO] Running command: blastn -query OceanDNA-b21693/markers.fasta -db /var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference/reference_markers.fasta -out OceanDNA-b21693/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:09,182] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:09,189] [INFO] Selected 6 target genomes.
[2023-03-17 09:59:09,190] [INFO] Target genome list was writen to OceanDNA-b21693/target_genomes.txt
[2023-03-17 09:59:09,281] [INFO] Task started: fastANI
[2023-03-17 09:59:09,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d08453b-3029-40f6-a1a6-c1681cedeb9e/OceanDNA-b21693.fa --refList OceanDNA-b21693/target_genomes.txt --output OceanDNA-b21693/fastani_result.tsv --threads 1
[2023-03-17 09:59:12,259] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:12,259] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:59:12,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:59:12,260] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:59:12,260] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:59:12,260] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-17 09:59:12,262] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21693/tc_result.tsv
[2023-03-17 09:59:12,267] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:59:12,267] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:59:12,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference/checkm_data
[2023-03-17 09:59:12,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:59:12,542] [INFO] Task started: CheckM
[2023-03-17 09:59:12,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21693/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21693/checkm_input OceanDNA-b21693/checkm_result
[2023-03-17 09:59:40,689] [INFO] Task succeeded: CheckM
[2023-03-17 09:59:40,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:59:40,855] [INFO] ===== Completeness check finished =====
[2023-03-17 09:59:40,855] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:59:40,855] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21693/markers.fasta)
[2023-03-17 09:59:40,857] [INFO] Task started: Blastn
[2023-03-17 09:59:40,857] [INFO] Running command: blastn -query OceanDNA-b21693/markers.fasta -db /var/lib/cwl/stg141140d9-324d-4337-97d5-00ba55629830/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21693/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:59:42,212] [INFO] Task succeeded: Blastn
[2023-03-17 09:59:42,220] [INFO] Selected 15 target genomes.
[2023-03-17 09:59:42,220] [INFO] Target genome list was writen to OceanDNA-b21693/target_genomes_gtdb.txt
[2023-03-17 09:59:42,606] [INFO] Task started: fastANI
[2023-03-17 09:59:42,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d08453b-3029-40f6-a1a6-c1681cedeb9e/OceanDNA-b21693.fa --refList OceanDNA-b21693/target_genomes_gtdb.txt --output OceanDNA-b21693/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:59:49,903] [INFO] Task succeeded: fastANI
[2023-03-17 09:59:49,903] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:59:49,904] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
--------------------------------------------------------------------------------
[2023-03-17 09:59:49,907] [INFO] GTDB search result was written to OceanDNA-b21693/result_gtdb.tsv
[2023-03-17 09:59:49,914] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:59:49,921] [INFO] DFAST_QC result json was written to OceanDNA-b21693/dqc_result.json
[2023-03-17 09:59:49,921] [INFO] DFAST_QC completed!
[2023-03-17 09:59:49,921] [INFO] Total running time: 0h0m49s